Comparative Mapping and Candidate Gene Analysis of SSIIa Associated with Grain Amylopectin Content in Barley ( Hordeum vulgare L.)

Amylopectin concentration in barley endosperm has important effects on grain quality and end-use. In this study, quantitative trait locus (QTL) analysis together with genome-wide association studies (GWAS) were performed to identify markers linked to grain amylopectin content respectively using a doubled haploid (DH) population of 178 lines and a collection of 185 diverse barley germplasms both genotyped by genotyping-by-sequencing (GBS). A stable QTL on chromosome 7H and 11 associated single nucleotide polymorphisms (SNPs) were detected. In the co-localized region, the ( ) gene was predicted as the candidate gene. Then we isolated and characterized biparental alleles of the DH population, investigated the expression pattern by quantitative real-time PCR (qRT-PCR), and revealed that a 33-bp deletion in exon 2 is responsible for reducing transcript, thus resulting in a reduced amylopectin content. A sequence-based molecular marker was developed for the allele and validated the effectivity, which would provide help for barley breeding.